X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAAFrequencyTest.java;h=646412f85ae4ad90f267fd5b5b453c52d8abe146;hb=96356075a122b745936738f478a8ee33ac7e0f0a;hp=bb3510a03700feeddd228bd8e680e234c6f22aa9;hpb=0a5ce6145bb76fc7eb8a5cc2670e20453fbedd29;p=jalview.git diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java index bb3510a..646412f 100644 --- a/test/jalview/analysis/AAFrequencyTest.java +++ b/test/jalview/analysis/AAFrequencyTest.java @@ -25,14 +25,32 @@ import static org.testng.AssertJUnit.assertNull; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; -import jalview.datamodel.Profile; +import jalview.datamodel.HiddenMarkovModel; +import jalview.datamodel.ProfileI; +import jalview.datamodel.ProfilesI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.gui.JvOptionPane; +import jalview.io.DataSourceType; +import jalview.io.FileParse; +import jalview.io.HMMFile; +import java.io.IOException; +import java.net.MalformedURLException; + +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class AAFrequencyTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = { "Functional" }) public void testCalculate_noProfile() { @@ -41,12 +59,12 @@ public class AAFrequencyTest SequenceI seq3 = new Sequence("Seq3", "C---G"); SequenceI seq4 = new Sequence("Seq4", "CA--t"); SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; - Profile[] result = new Profile[seq1.getLength()]; - - AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false); + int width = seq1.getLength(); + ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, + false); // col 0 is 100% C - Profile col = result[0]; + ProfileI col = result.get(0); assertEquals(100f, col.getPercentageIdentity(false)); assertEquals(100f, col.getPercentageIdentity(true)); assertEquals(4, col.getMaxCount()); @@ -54,28 +72,28 @@ public class AAFrequencyTest assertNull(col.getCounts()); // col 1 is 75% A - col = result[1]; + col = result.get(1); assertEquals(75f, col.getPercentageIdentity(false)); assertEquals(100f, col.getPercentageIdentity(true)); assertEquals(3, col.getMaxCount()); assertEquals("A", col.getModalResidue()); // col 2 is 50% G 50% C or 25/25 counting gaps - col = result[2]; + col = result.get(2); assertEquals(25f, col.getPercentageIdentity(false)); assertEquals(50f, col.getPercentageIdentity(true)); assertEquals(1, col.getMaxCount()); assertEquals("CG", col.getModalResidue()); // col 3 is all gaps - col = result[3]; + col = result.get(3); assertEquals(0f, col.getPercentageIdentity(false)); assertEquals(0f, col.getPercentageIdentity(true)); assertEquals(0, col.getMaxCount()); assertEquals("", col.getModalResidue()); // col 4 is 75% T 25% G - col = result[4]; + col = result.get(4); assertEquals(75f, col.getPercentageIdentity(false)); assertEquals(75f, col.getPercentageIdentity(true)); assertEquals(3, col.getMaxCount()); @@ -90,26 +108,27 @@ public class AAFrequencyTest SequenceI seq3 = new Sequence("Seq3", "C--G"); SequenceI seq4 = new Sequence("Seq4", "CA-t"); SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; - Profile[] result = new Profile[seq1.getLength()]; + int width = seq1.getLength(); + ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, + true); - AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true); - Profile profile = result[0]; + ProfileI profile = result.get(0); assertEquals(4, profile.getCounts().getCount('C')); assertEquals(4, profile.getHeight()); assertEquals(4, profile.getNonGapped()); - profile = result[1]; + profile = result.get(1); assertEquals(3, profile.getCounts().getCount('A')); assertEquals(4, profile.getHeight()); assertEquals(3, profile.getNonGapped()); - profile = result[2]; + profile = result.get(2); assertEquals(1, profile.getCounts().getCount('C')); assertEquals(1, profile.getCounts().getCount('G')); assertEquals(4, profile.getHeight()); assertEquals(2, profile.getNonGapped()); - profile = result[3]; + profile = result.get(3); assertEquals(3, profile.getCounts().getCount('T')); assertEquals(1, profile.getCounts().getCount('G')); assertEquals(4, profile.getHeight()); @@ -124,15 +143,16 @@ public class AAFrequencyTest SequenceI seq3 = new Sequence("Seq3", "C--G"); SequenceI seq4 = new Sequence("Seq4", "CA-t"); SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; - Profile[] result = new Profile[seq1.getLength()]; - // ensure class loaded and initialized - AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true); + // ensure class loaded and initialised + int width = seq1.getLength(); + AAFrequency.calculate(seqs, width, 0, width, true); + int reps = 100000; long start = System.currentTimeMillis(); for (int i = 0; i < reps; i++) { - AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true); + AAFrequency.calculate(seqs, width, 0, width, true); } System.out.println(System.currentTimeMillis() - start); } @@ -154,11 +174,11 @@ public class AAFrequencyTest SequenceI seq3 = new Sequence("Seq3", "C---G"); SequenceI seq4 = new Sequence("Seq4", "CA--t"); SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; - Profile[] profiles = new Profile[seq1.getLength()]; - AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true); + int width = seq1.getLength(); + ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true); AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus", - "PID", new Annotation[seq1.getLength()]); + "PID", new Annotation[width]); AAFrequency .completeConsensus(consensus, profiles, 0, 5, false, true, 4); @@ -195,11 +215,11 @@ public class AAFrequencyTest SequenceI seq3 = new Sequence("Seq3", "C---G"); SequenceI seq4 = new Sequence("Seq4", "CA--t"); SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 }; - Profile[] profiles = new Profile[seq1.getLength()]; - AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true); + int width = seq1.getLength(); + ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true); AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus", - "PID", new Annotation[seq1.getLength()]); + "PID", new Annotation[width]); AAFrequency .completeConsensus(consensus, profiles, 0, 5, true, false, 4); @@ -219,4 +239,45 @@ public class AAFrequencyTest assertEquals("T 75%", ann.description); assertEquals("T", ann.displayCharacter); } + + @Test(groups = { "Functional" }) + public void testGetHMMProfileFor() + throws MalformedURLException, IOException + { + + HMMFile hmmFile = new HMMFile(new FileParse( + "test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE)); + hmmFile.parse(); + HiddenMarkovModel hmm = hmmFile.getHMM(); + AlignmentAnnotation aa = hmm.createAnnotation(80); + aa.setHMM(hmm); + + int[] expected = { 0, 4, 100, 'T', 71, 'C', 12, 'G', 9, 'A', 9 }; + int[] actual = AAFrequency.getHMMProfileFor(aa, 17, false); + for (int i = 0; i < actual.length; i++) + { + if (i == 2) + { + assertEquals(actual[i], expected[i], 5); + } + else + { + assertEquals(actual[i], expected[i], 1); + } + } + + int[] expected2 = { 0, 4, 85, 'A', 85, 'C', 0, 'G', 0, 'T', 0 }; + int[] actual2 = AAFrequency.getHMMProfileFor(aa, 2, true); + for (int i = 0; i < actual.length; i++) + { + if (i == 2) + { + assertEquals(actual[i], expected[i], 5); + } + else + { + assertEquals(actual[i], expected[i], 1); + } + } + } }